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Zhang Z, Zhang H, Liu J, Chen K, Wang Y, Zhang G, Li L, Yue H, Weng Y, Li Y, Chen P. The mutation of CsSUN, an IQD family protein, is responsible for the short and fat fruit (sff) in cucumber (Cucumis sativus L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112177. [PMID: 38964612 DOI: 10.1016/j.plantsci.2024.112177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/20/2024] [Accepted: 06/30/2024] [Indexed: 07/06/2024]
Abstract
The fruit shape of cucumber is an important agronomic trait, and mining regulatory genes, especially dominant ones, is vital for cucumber breeding. In this study, we identified a short and fat fruit mutant, named sff, from an EMS mutagenized population. Compared to the CCMC (WT), sff (MT) exhibited reduced fruit length and increased dimeter. Segregation analysis revealed that the sff phenotype is controlled by a semi-dominant single gene with dosage effects. Through map-based cloning, the SFF locus was narrowed down to a 52.6 kb interval with two SNPs (G651A and C1072T) in the second and third exons of CsaV3_1G039870, which encodes an IQD family protein, CsSUN. The G651A within the IQ domain of CsSUN was identified as the unique SNP among 114 cucumber accessions, and it was the primary cause of the functional alteration in CsSUN. By generating CsSUN knockout lines in cucumber, we confirmed that CsSUN was responsible for sff mutant phenotype. The CsSUN is localized to the plasma membrane. CsSUN exhibited the highest expression in the fruit with lower expression in sff compared to WT. Histological observations suggest that the sff mutant phenotype is due to increased transverse cell division and inhibited longitudinal cell division. Transcriptome analysis revealed that CsSUN significantly affected the expression of genes related to cell division, expansion, and auxin signal transduction. This study unveils CsSUN's crucial role in shaping cucumber fruit and offers novel insights for cucumber breeding.
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Affiliation(s)
- Zhengao Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Haiqiang Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junyan Liu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kang Chen
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yixin Wang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gaoyuan Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Lixia Li
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Hongzhong Yue
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China
| | - Yiqun Weng
- USDA-ARS Vegetable Crops Research Unit, University of Wisconsin, Madison, WI 53706, USA
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Peng Chen
- College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Wang B, Liu X, Li Z, Zeng K, Guo J, Xin T, Zhang Z, Li JF, Yang X. A nuclease-dead Cas9-derived tool represses target gene expression. PLANT PHYSIOLOGY 2024; 195:1880-1892. [PMID: 38478589 DOI: 10.1093/plphys/kiae149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/24/2024] [Indexed: 06/30/2024]
Abstract
Manipulation of gene expression is central to understanding gene function, engineering cell behavior, and altering biological traits according to production demands. Nuclease-dead Cas9 (dCas9), a variant of active Cas9, offers a versatile platform for the precise control of genome function without DNA cleavage. Notably, however, an effective and universal dCas9-based transcriptional repression system remains unavailable in plants. The noncanonical histone acetyltransferase TENDRIL-LESS (CsTEN) is responsible for chromatin loosening and histone modification in cucumber (Cucumis sativus). In this study, we engineered a gene regulation tool by fusing TEN and its truncated proteins with dCas9. The full-length dCas9-TEN protein substantially repressed gene expression, with the N-terminal domain identified as the core repression domain. We subsequently validated the specificity and efficacy of this system through both transient infection and genetic transformation in cucumber and Arabidopsis (Arabidopsis thaliana). The electrophoretic mobility shift assay (EMSA) revealed the ability of the N-terminal domain of TEN to bind to chromatin, which may promote target binding of the dCas9 complex and enhance the transcriptional repression effect. Our tool enriches the arsenal of genetic regulation tools available for precision breeding in crops.
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Affiliation(s)
- Bowen Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xiaolin Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhenxiang Li
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Kang Zeng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Horticulture, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiangyi Guo
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Tongxu Xin
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhen Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng 475004, China
| | - Jian-Feng Li
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xueyong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Sun Y, Yang H, Ren T, Zhao J, Lang X, Nie L, Zhao W. CmERF1 acts as a positive regulator of fruits and leaves growth in melon (Cucumis melo L.). PLANT MOLECULAR BIOLOGY 2024; 114:70. [PMID: 38842600 DOI: 10.1007/s11103-024-01468-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/14/2024] [Indexed: 06/07/2024]
Abstract
Melon (Cucumis melo L.) is an important horticultural and economic crop. ETHYLENE RESPONSE FACTOR1 (ERF1) plays an important role in regulating plant development, and the resistance to multiple biotic and abiotic stresses. In this study, developmental biology, molecular biology and biochemical assays were performed to explore the biological function of CmERF1 in melon. Abundant transcripts of CmERF1 were found in ovary at green-yellow bud (GYB) and rapid enlargement (ORE) stages. In CmERF1 promoter, the cis-regulatory elements for indoleacetic acid (IAA), methyl jasmonate (MeJA), salicylic acid (SA), abscisic acid (ABA), gibberellic acid (GA), light and low temperature responses were found. CmERF1 could be significantly induced by ethylene, IAA, MeJA, SA, ABA, and respond to continuous light and low temperature stresses in melon. Ectopic expression of CmERF1 increased the length of siliqua and carpopodium, and expanded the size of leaves in Arabidopsis. Knockdown of CmERF1 led to smaller ovary at anthesis, mature fruit and leaves in melon. In CmERF1-RNAi #2 plants, 75 genes were differently expressed compared with control, and the promoter regions of 28 differential expression genes (DEGs) contained the GCC-box (AGCCGCC) or DRE (A/GCCGAC) cis-acting elements of CmERF1. A homolog of cell division cycle protein 48 (CmCDC48) was proved to be the direct target of CmERF1 by the yeast one-hybrid assay and dual-luciferase (LUC) reporter (DLR) system. These results indicated that CmERF1 was able to promote the growth of fruits and leaves, and involved in multiple hormones and environmental signaling pathways in melon.
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Affiliation(s)
- Yufan Sun
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Haiming Yang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Tiantian Ren
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Jiateng Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Xinmei Lang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China
| | - Lanchun Nie
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China.
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, Hebei, 071000, China.
- Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, Baoding, Hebei, 071000, China.
| | - Wensheng Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, 071000, China.
- Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, Hebei, 071000, China.
- Ministry of Education of China-Hebei Province Joint Innovation Center for Efficient Green Vegetable Industry, Baoding, Hebei, 071000, China.
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Sojka J, Šamajová O, Šamaj J. Gene-edited protein kinases and phosphatases in molecular plant breeding. TRENDS IN PLANT SCIENCE 2024; 29:694-710. [PMID: 38151445 DOI: 10.1016/j.tplants.2023.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/07/2023] [Accepted: 11/29/2023] [Indexed: 12/29/2023]
Abstract
Protein phosphorylation, the most common and essential post-translational modification, belongs to crucial regulatory mechanisms in plants, affecting their metabolism, intracellular transport, cytoarchitecture, cell division, growth, development, and interactions with the environment. Protein kinases and phosphatases, two important families of enzymes optimally regulating phosphorylation, have now become important targets for gene editing in crops. We review progress on gene-edited protein kinases and phosphatases in crops using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9). We also provide guidance for computational prediction of alterations and/or changes in function, activity, and binding of protein kinases and phosphatases as consequences of CRISPR/Cas9-based gene editing with its possible application in modern crop molecular breeding towards sustainable agriculture.
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Affiliation(s)
- Jiří Sojka
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Olga Šamajová
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Biotechnology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 783 71 Olomouc, Czech Republic.
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Ma M, Yang L, Hu Z, Mo C, Geng S, Zhao X, He Q, Xiao L, Lu L, Wang D, Li S, Kong Q, Li D, Bie Z. Multiplex gene editing reveals cucumber MILDEW RESISTANCE LOCUS O family roles in powdery mildew resistance. PLANT PHYSIOLOGY 2024; 195:1069-1088. [PMID: 38330431 DOI: 10.1093/plphys/kiae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 02/10/2024]
Abstract
Powdery mildew (PM) is one of the most widespread and prevalent diseases that affects a wide range of crops. In cucumber (Cucumis sativus L.), previous forward genetic studies have identified MILDEW RESISTANCE LOCUS O 8 (CsMLO8) as necessary but alone insufficient for cucumber PM resistance (PMR) and suggested the involvement of other members of the CsMLO family. However, the function of other CsMLO family members in cucumber remains largely unknown. Here, we developed a highly efficient multiplex gene editing system in cucumber to generate a series of Csmlo mutants from all the 13 family members. Systematic analysis of these mutants revealed growth effects of these CsMLO family members on development and PMR. Importantly, we obtained the Csmlo1/8/11 triple mutant with complete resistance to PM. Transcriptome and proteome analysis of PM-resistant Csmlo mutants suggested that the kinesin-like calmodulin-binding protein (KCBP)-interacting Ca2+-binding protein (CsKIC), calmodulin-like protein 28 (CsCML28), and Ca2+-dependent protein kinase 11 (CsCPK11)-mediated calcium signaling pathway is involved in PMR. CsMLO8 interacted directly with CsKIC, and the simultaneous silencing of both genes resulted in a phenotype that resembled the silencing of CsKIC alone. Silencing CsCML28 and CsCPK11 increased susceptibility to PM, whereas overexpressing CsCPK11 through genetic transformation enhanced cucumber's PMR, demonstrating their positive regulatory roles in PMR. Given the importance of PMR for cucurbit crops, this research provides unprecedented insights into the function of the proteins encoded by the CsMLO gene family as well as the plant defense response to PM pathogen.
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Affiliation(s)
- Mingru Ma
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Yang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenzhu Hu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Changjuan Mo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Shouyu Geng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Zhao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiuyu He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Xiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Liurong Lu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Shanggui Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiusheng Kong
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Dawei Li
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Zhilong Bie
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Department of Science and Technology of Hubei Province, Wuhan 430070, China
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Wang M, Jiang N, Xu Y, Chen X, Wang C, Wang C, Wang S, Xu K, Chai S, Yu Q, Zhang Z, Zhang H. CmBr confers fruit bitterness under CPPU treatment in melon. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38816932 DOI: 10.1111/pbi.14399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 04/06/2024] [Accepted: 05/13/2024] [Indexed: 06/01/2024]
Abstract
Many biotic or abiotic factors such as CPPU (N-(2-chloro-pyridin-4-yl)-N'-phenylurea), a growth regulator of numerous crops, can induce bitterness in cucurbits. In melon, cucurbitacin B is the major compound leading to bitterness. However, the molecular mechanism underlying CuB biosynthesis in response to different conditions remains unclear. Here, we identified a set of genes involved in CPPU-induced CuB biosynthesis in melon fruit and proposed CmBr gene as the major regulator. Using CRISPR/Cas9 gene editing, we confirmed CmBr's role in regulating CuB biosynthesis under CPPU treatment. We further discovered a CPPU-induced MYB-related transcription factor, CmRSM1, which specifically binds to the Myb motif within the CmBr promoter and activates its expression. Moreover, we developed an introgression line by introducing the mutated Cmbr gene into an elite variety and eliminated CPPU-induced bitterness, demonstrating its potential application in breeding. This study offers a valuable tool for breeding high-quality non-bitter melon varieties and provides new insights into the regulation of secondary metabolites under environmental stresses.
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Affiliation(s)
- Mingyan Wang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Naiyu Jiang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yuanchao Xu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xinxiu Chen
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Cui Wang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chuangjiang Wang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shiqi Wang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Kuipeng Xu
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Sen Chai
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qing Yu
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Huimin Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs, National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao), College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
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7
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Xin H, Liu X, Chai S, Yang X, Li H, Wang B, Xu Y, Lin S, Zhong X, Liu B, Lu Z, Zhang Z. Identification and functional characterization of conserved cis-regulatory elements responsible for early fruit development in cucurbit crops. THE PLANT CELL 2024; 36:2272-2288. [PMID: 38421027 PMCID: PMC11132967 DOI: 10.1093/plcell/koae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 03/02/2024]
Abstract
A number of cis-regulatory elements (CREs) conserved during evolution have been found to be responsible for phenotypic novelty and variation. Cucurbit crops such as cucumber (Cucumis sativus), watermelon (Citrullus lanatus), melon (Cucumis melo), and squash (Cucurbita maxima) develop fruits from an inferior ovary and share some similar biological processes during fruit development. Whether conserved regulatory sequences play critical roles in fruit development of cucurbit crops remains to be explored. In six well-studied cucurbit species, we identified 392,438 conserved noncoding sequences (CNSs), including 82,756 that are specific to cucurbits, by comparative genomics. Genome-wide profiling of accessible chromatin regions (ACRs) and gene expression patterns mapped 20,865 to 43,204 ACRs and their potential target genes for two fruit tissues at two key developmental stages in six cucurbits. Integrated analysis of CNSs and ACRs revealed 4,431 syntenic orthologous CNSs, including 1,687 cucurbit-specific CNSs that overlap with ACRs that are present in all six cucurbit crops and that may regulate the expression of 757 adjacent orthologous genes. CRISPR mutations targeting two CNSs present in the 1,687 cucurbit-specific sequences resulted in substantially altered fruit shape and gene expression patterns of adjacent NAC1 (NAM, ATAF1/2, and CUC2) and EXT-like (EXTENSIN-like) genes, validating the regulatory roles of these CNSs in fruit development. These results not only provide a number of target CREs for cucurbit crop improvement, but also provide insight into the roles of CREs in plant biology and during evolution.
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Affiliation(s)
- Hongjia Xin
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Xin Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sen Chai
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Xueyong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Bowen Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yuanchao Xu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shengnan Lin
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan 430070, China
| | - Xiaoyun Zhong
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bin Liu
- Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi 830091China
| | - Zefu Lu
- National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
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8
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Pan J, Song J, Sohail H, Sharif R, Yan W, Hu Q, Qi X, Yang X, Xu X, Chen X. RNA-seq-based comparative transcriptome analysis reveals the role of CsPrx73 in waterlogging-triggered adventitious root formation in cucumber. HORTICULTURE RESEARCH 2024; 11:uhae062. [PMID: 38659441 PMCID: PMC11040206 DOI: 10.1093/hr/uhae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 02/18/2024] [Indexed: 04/26/2024]
Abstract
Abiotic stressors like waterlogging are detrimental to cucumber development and growth. However, comprehension of the highly complex molecular mechanism underlying waterlogging can provide an opportunity to enhance cucumber tolerance under waterlogging stress. We examined the hypocotyl and stage-specific transcriptomes of the waterlogging-tolerant YZ026A and the waterlogging-sensitive YZ106A, which had different adventitious rooting ability under waterlogging. YZ026A performed better under waterlogging stress by altering its antioxidative machinery and demonstrated a greater superoxide ion (O 2-) scavenging ability. KEGG pathway enrichment analysis showed that a high number of differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis. By pairwise comparison and weighted gene co-expression network analysis analysis, 2616 DEGs were obtained which were categorized into 11 gene co-expression modules. Amongst the 11 modules, black was identified as the common module and yielded a novel key regulatory gene, CsPrx73. Transgenic cucumber plants overexpressing CsPrx73 enhance adventitious root (AR) formation under waterlogging conditions and increase reactive oxygen species (ROS) scavenging. Silencing of CsPrx73 expression by virus-induced gene silencing adversely affects AR formation under the waterlogging condition. Our results also indicated that CsERF7-3, a waterlogging-responsive ERF transcription factor, can directly bind to the ATCTA-box motif in the CsPrx73 promoter to initiate its expression. Overexpression of CsERF7-3 enhanced CsPrx73 expression and AR formation. On the contrary, CsERF7-3-silenced plants decreased CsPrx73 expression and rooting ability. In conclusion , our study demonstrates a novel CsERF7-3-CsPrx73 module that allows cucumbers to adapt more efficiently to waterlogging stress by promoting AR production and ROS scavenging.
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Affiliation(s)
- Jiawei Pan
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jia Song
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Hamza Sohail
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Rahat Sharif
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Wenjing Yan
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Qiming Hu
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xiaohua Qi
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xiaodong Yang
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xuewen Xu
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute ofVegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Xuehao Chen
- Department of Horticulture, School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute ofVegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
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9
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Prado GS, Rocha DC, dos Santos LN, Contiliani DF, Nobile PM, Martinati-Schenk JC, Padilha L, Maluf MP, Lubini G, Pereira TC, Monteiro-Vitorello CB, Creste S, Boscariol-Camargo RL, Takita MA, Cristofani-Yaly M, de Souza AA. CRISPR technology towards genome editing of the perennial and semi-perennial crops citrus, coffee and sugarcane. FRONTIERS IN PLANT SCIENCE 2024; 14:1331258. [PMID: 38259920 PMCID: PMC10801916 DOI: 10.3389/fpls.2023.1331258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024]
Abstract
Gene editing technologies have opened up the possibility of manipulating the genome of any organism in a predicted way. CRISPR technology is the most used genome editing tool and, in agriculture, it has allowed the expansion of possibilities in plant biotechnology, such as gene knockout or knock-in, transcriptional regulation, epigenetic modification, base editing, RNA editing, prime editing, and nucleic acid probing or detection. This technology mostly depends on in vitro tissue culture and genetic transformation/transfection protocols, which sometimes become the major challenges for its application in different crops. Agrobacterium-mediated transformation, biolistics, plasmid or RNP (ribonucleoprotein) transfection of protoplasts are some of the commonly used CRISPR delivery methods, but they depend on the genotype and target gene for efficient editing. The choice of the CRISPR system (Cas9, Cas12), CRISPR mechanism (plasmid or RNP) and transfection technique (Agrobacterium spp., PEG solution, lipofection) directly impacts the transformation efficiency and/or editing rate. Besides, CRISPR/Cas technology has made countries rethink regulatory frameworks concerning genetically modified organisms and flexibilize regulatory obstacles for edited plants. Here we present an overview of the state-of-the-art of CRISPR technology applied to three important crops worldwide (citrus, coffee and sugarcane), considering the biological, methodological, and regulatory aspects of its application. In addition, we provide perspectives on recently developed CRISPR tools and promising applications for each of these crops, thus highlighting the usefulness of gene editing to develop novel cultivars.
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Affiliation(s)
- Guilherme Souza Prado
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
| | - Dhiôvanna Corrêia Rocha
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
- Institute of Biology, State University of Campinas (Unicamp), Campinas, Brazil
| | - Lucas Nascimento dos Santos
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
- Institute of Biology, State University of Campinas (Unicamp), Campinas, Brazil
| | - Danyel Fernandes Contiliani
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Paula Macedo Nobile
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
| | | | - Lilian Padilha
- Coffee Center of the Agronomic Institute of Campinas (IAC), Campinas, Brazil
- Embrapa Coffee, Brazilian Agricultural Research Corporation, Brasília, Federal District, Brazil
| | - Mirian Perez Maluf
- Coffee Center of the Agronomic Institute of Campinas (IAC), Campinas, Brazil
- Embrapa Coffee, Brazilian Agricultural Research Corporation, Brasília, Federal District, Brazil
| | - Greice Lubini
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Tiago Campos Pereira
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | | | - Silvana Creste
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | | | - Marco Aurélio Takita
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
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10
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Chen X, He S, Wang Z, Zhai Y, Guo W, Li X. Production of transgenic periclinal chimeras in pumpkin - a tool for revealing cell fates of L1 meristem. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:126-139. [PMID: 37975550 DOI: 10.1111/plb.13593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
Genetic engineering is commonly used to improve the agronomic traits of crops. However, genetic transformation in pumpkin remains a challenge. Conducting transformation trials, we accidentally created transgenic L1 periclinal chimeras in pumpkins. Using our modified Agrobacterium-mediated transformation, we generated transgenic L1 periclinal chimeras which have high value in research on development of the meristem. Fluorescence observations of transformed L1 cells enabled us to reveal cell fates. These L1 cells can develop into stomata, epidermal hairs, seed coat, and epidermis of the root, stem, leaf, flower, and fruit. These periclinal chimeras can be propagated vegetatively with minimal risk of transgene flow. This study offers new perspectives on development of the meristem and a promising technique for creating transgenic periclinal chimeras in plants.
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Affiliation(s)
- X Chen
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, Henan, China
| | - S He
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Z Wang
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Y Zhai
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, Henan, China
| | - W Guo
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, Henan, China
| | - X Li
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, Henan, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, Henan, China
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11
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Zhou L, Tian Y, Ren L, Yan Z, Jiang J, Shi Q, Geng C, Li X. A natural substitution of a conserved amino acid in eIF4E confers resistance against multiple potyviruses. MOLECULAR PLANT PATHOLOGY 2024; 25:e13418. [PMID: 38279849 PMCID: PMC10777747 DOI: 10.1111/mpp.13418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/29/2024]
Abstract
Eukaryotic translation initiation factor 4E (eIF4E), which plays a pivotal role in initiating translation in eukaryotic organisms, is often hijacked by the viral genome-linked protein to facilitate the infection of potyviruses. In this study, we found that the naturally occurring amino acid substitution D71G in eIF4E is widely present in potyvirus-resistant watermelon accessions and disrupts the interaction between watermelon eIF4E and viral genome-linked protein of papaya ringspot virus-watermelon strain, zucchini yellow mosaic virus or watermelon mosaic virus. Multiple sequence alignment and protein modelling showed that the amino acid residue D71 located in the cap-binding pocket of eIF4E is strictly conserved in many plant species. The mutation D71G in watermelon eIF4E conferred resistance against papaya ringspot virus-watermelon strain and zucchini yellow mosaic virus, and the equivalent mutation D55G in tobacco eIF4E conferred resistance to potato virus Y. Therefore, our finding provides a potential precise target for breeding plants resistant to multiple potyviruses.
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Affiliation(s)
- Ling‐Xi Zhou
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Yan‐Ping Tian
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Li‐Li Ren
- Science and Technology Research Center of China CustomsBeijingChina
| | - Zhi‐Yong Yan
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Jun Jiang
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Qing‐Hua Shi
- College of Horticulture Science and EngineeringShandong Agricultural UniversityTai'anChina
| | - Chao Geng
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
| | - Xiang‐Dong Li
- Shandong Provincial Key Laboratory of Agricultural Microbiology, Department of Plant Pathology, College of Plant ProtectionShandong Agricultural UniversityTai'anChina
- Institute of Plant ProtectionShandong Academy of Agricultural SciencesJi'nanChina
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12
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Ma K, Yuan Y, Fang C. Mainstreaming production and nutrient resilience of vegetable crops in megacities: pre-breeding for terrace cultivation. FRONTIERS IN PLANT SCIENCE 2023; 14:1237099. [PMID: 38053771 PMCID: PMC10694833 DOI: 10.3389/fpls.2023.1237099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/30/2023] [Indexed: 12/07/2023]
Abstract
Modern megacities offer convenient lifestyles to their citizens. However, agriculture is becoming increasingly vulnerable, especially during unexpected public health emergencies such as pandemics. Fortunately, the adaptability of terrace vegetables cultivation presents an opportunity to grow horticultural crops in residential spaces, bringing numerous benefits to citizens, including enhanced nutrition and recreational engagement in the cultivation process. Although certain planting skills and equipment have been developed, the citizens tend to sow some seeds with unknown pedigree, it is rare to find new plant varieties specifically bred for cultivation as terrace vegetables. To expand the genetic basis of new breeding materials, elite parents, and varieties (pre-breeding) for terrace cultivation, this review not only discusses the molecular breeding strategy for the identification, creation, and application of rational alleles for improving horticultural characteristics including plant architecture, flavor quality, and ornamental character, but also assesses the potential for terrace cultivation of some representative vegetable crops. We conclude that the process of pre-breeding specifically for terrace cultivation environments is vital for generating a genetic basis for urban terrace vegetable crops.
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13
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Tian S, Zhang Z, Qin G, Xu Y. Parthenocarpy in Cucurbitaceae: Advances for Economic and Environmental Sustainability. PLANTS (BASEL, SWITZERLAND) 2023; 12:3462. [PMID: 37836203 PMCID: PMC10574560 DOI: 10.3390/plants12193462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
Parthenocarpy is an important agricultural trait that not only produces seedless fruits, but also increases the rate of the fruit set under adverse environmental conditions. The study of parthenocarpy in Cucurbitaceae crops has considerable implications for cultivar improvement. This article provides a comprehensive review of relevant studies on the parthenocarpic traits of several major Cucurbitaceae crops and offers a perspective on future developments and research directions.
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Affiliation(s)
- Shouwei Tian
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
| | - Zeliang Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Genji Qin
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yong Xu
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China
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14
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Wan L, Wang Z, Zhang X, Zeng H, Ren J, Zhang N, Sun Y, Mi T. Optimised Agrobacterium-Mediated Transformation and Application of Developmental Regulators Improve Regeneration Efficiency in Melons. Genes (Basel) 2023; 14:1432. [PMID: 37510336 PMCID: PMC10378916 DOI: 10.3390/genes14071432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/27/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Melon (Cucumis melo L.) is a protected crop in China with high economic value. Agrobacterium-mediated genetic transformation is a powerful tool to improve agronomic traits and obtain elite germplasm. However, current transformation protocols in melons are inefficient and highly genotype-dependent. To improve transformation in melon, we tested different infiltration methods for Agrobacterium-mediated transformation. Among these methods, micro-brushing and sonication for 20 s, followed by vacuum infiltration at -1.0 kPa for 90 s, resulted in the strongest green fluorescent protein signal and increased the proportion of infected explants. We transformed melon with developmental regulatory genes AtGRF5, AtPLT5, AtBBM, AtWUS, AtWOX5, and AtWIND1 from Arabidopsis and estimated regeneration frequencies as the number of regenerating shoots/total number of inoculated explants in the selection medium. The overexpression of AtGRF5 and AtPLT5 in melon resulted in transformation efficiencies of 42.3% and 33% in ZHF and 45.6% and 32.9% in Z12, respectively, which were significantly higher than those of the control. AtGRF5 and AtPLT5 expression cassettes were added to CRISPR/Cas9 genome-editing vectors to obtain transgenic phytoene desaturase CmPDS knockout mutants. Using AtGRF5 or AtPLT5, multi-allelic mutations were observed at CmPDS target sites in recalcitrant melon genotypes. This strategy enables genotype-flexible transformation and promotes precise genome modification technologies in melons.
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Affiliation(s)
- Lili Wan
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Zhuanrong Wang
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Xuejun Zhang
- Research Center of Hami Melon, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- Hainan Sanya Crops Breeding Trial Center, Xinjiang Academy of Agricultural Sciences, Sanya 572019, China
| | - Hongxia Zeng
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Jian Ren
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Na Zhang
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Yuhong Sun
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Tang Mi
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
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15
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Liu Y, Li Y, Guo H, Lv B, Feng J, Wang H, Zhang Z, Chai S. Gibberellin biosynthesis is required for CPPU-induced parthenocarpy in melon. HORTICULTURE RESEARCH 2023; 10:uhad084. [PMID: 37323228 PMCID: PMC10266944 DOI: 10.1093/hr/uhad084] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/18/2023] [Indexed: 06/17/2023]
Abstract
Spraying N-(2-chloro-4-pyridyl)-N'-phenylurea (CPPU), an exogenous cytokinin (CK) growth regulator, is the conventional method for inducing fruit set during melon (Cucumis melo L.) production; however, the mechanism by which CPPU induces fruit set is unclear. Through histological and morphological observations, fruit size was comparable between CPPU-induced fruits and normal pollinated fruits because CPPU-induced fruits had higher cell density but smaller cell size compared with normal pollinated fruits. CPPU promotes the accumulation of gibberellin (GA) and auxin and decreases the level of abscisic acid (ABA) during fruit set. Moreover, application of the GA inhibitor paclobutrazol (PAC) partially inhibits CPPU-induced fruit set. Transcriptome analysis revealed that CPPU-induced fruit set specifically induced the GA-related pathway, in which the key synthase encoding gibberellin 20-oxidase 1 (CmGA20ox1) was specifically upregulated. Further study indicated that the two-component response regulator 2 (CmRR2) of the cytokinin signaling pathway, which is highly expressed at fruit setting, positively regulates the expression of CmGA20ox1. Collectively, our study determined that CPPU-induced melon fruit set is dependent on GA biosynthesis, providing a theoretical basis for the creation of parthenocarpic melon germplasm.
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Affiliation(s)
| | | | | | - Bingsheng Lv
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Jing Feng
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Huihui Wang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | | | - Sen Chai
- Corresponding authors: E-mail: ;
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16
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Wei R, Zhang W, Li C, Hao Z, Huang D, Zhang W, Pan X. Establishment of Agrobacterium-mediated transformation system to Juglans sigillata Dode 'Qianhe-7'. Transgenic Res 2023; 32:193-207. [PMID: 37118332 DOI: 10.1007/s11248-023-00348-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 04/04/2023] [Indexed: 04/30/2023]
Abstract
An efficient genetic transformation system is of great significance for verifying gene function and improving plant breeding efficiency by gene engineering. In this study, a stable Agrobacterium mediated genetic transformation system of Juglans sigillata Dode 'Qianhe-7' was investigated using callus and negative pressure-assisted and ultrasonic-assisted transformation selection. The results showed that the axillary shoot leaves were suitable to induce callus and the callus proliferation rate could reach 516.27% when induction calli were cultured on DKW medium containing 0.5 mg L-1 indole-3-butyric acid, 1.2 mg L-1 2,4-dichlorophenoxyacetic acid and 0.5 mg L-1 kinetin for 18 d. In addition, negative pressure infection was the optimal infection method with the lowest browning rate (0.00%), high GFP conversion rate (16.67%), and better growth status. To further prove the feasibility of this genetic transformation system, the flavonol synthetase (JsFLS5) gene was successfully transformed into the into leaf-derived callus of 'Qianhe-7'. JsFLS5 expression and the content of total flavonoids in transformed callus were improved significantly compared with the untransformed callus, which proved that we had an efficient and reliable genetic transformation system using leaf-derived callus of Juglans sigillata.
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Affiliation(s)
- Rong Wei
- Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang, China
- College of Agricultural, Guizhou University, Guiyang, 550025, China
| | - Wen'e Zhang
- College of Agricultural, Guizhou University, Guiyang, 550025, China
| | - Chunxiang Li
- Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang, China
- College of Agricultural, Guizhou University, Guiyang, 550025, China
| | - Zhenkun Hao
- Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang, China
- College of Agricultural, Guizhou University, Guiyang, 550025, China
| | - Dong Huang
- Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang, China
- College of Agricultural, Guizhou University, Guiyang, 550025, China
| | - Wenlong Zhang
- Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang, China
- College of Agricultural, Guizhou University, Guiyang, 550025, China
| | - Xuejun Pan
- Guizhou Engineering Research Center for Fruit Crops, Guizhou University, Guiyang, China.
- College of Agricultural, Guizhou University, Guiyang, 550025, China.
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17
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Shams M, Khadivi A. Mechanisms of salinity tolerance and their possible application in the breeding of vegetables. BMC PLANT BIOLOGY 2023; 23:139. [PMID: 36915096 PMCID: PMC10012490 DOI: 10.1186/s12870-023-04152-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND In dry and semi-arid areas, salinity is the most serious hazard to agriculture, which can affect plant growth and development adversely. Over-accumulation of Na+ in plant organs can cause an osmotic effect and an imbalance in nutrient uptake. However, its harmful impact can vary depending on genotype, period of exposure to stress, plant development stage, and concentration and content of salt. To overcome the unfavorable effect of salinity, plants have developed two kinds of tolerance strategies based on either minimizing the entrance of salts by the roots or administering their concentration and diffusion. RESULTS Having sufficient knowledge of Na+ accumulation mechanisms and an understanding of the function of genes involved in transport activity will present a new option to enhance the salinity tolerance of vegetables related to food security in arid regions. Considerable improvements in tolerance mechanisms can be employed for breeding vegetables with boosted yield performance under salt stress. A conventional breeding method demands exhaustive research work in crops, while new techniques of molecular breeding, such as cutting-edge molecular tools and CRISPR technology are now available in economically important vegetables and give a fair chance for the development of genetically modified organisms. CONCLUSIONS Therefore, this review highlights the molecular mechanisms of salinity tolerance, various molecular methods of breeding, and many sources of genetic variation for inducing tolerance to salinity stress.
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Affiliation(s)
- Mostafakamal Shams
- Department of Plant Physiology and Biotechnology, Faculty of Biology, University of Gdansk, Gdansk, Poland.
| | - Ali Khadivi
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, Arak University, 38156-8-8349, Arak, Iran.
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18
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Chen F, Yong J, Zhang G, Liu M, Wang Q, Zhong H, Pan Y, Chen P, Weng Y, Li Y. An LTR retrotransposon insertion inside CsERECTA for an LRR receptor-like serine/threonine-protein kinase results in compact (cp) plant architecture in cucumber. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:31. [PMID: 36894705 DOI: 10.1007/s00122-023-04273-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/26/2022] [Indexed: 06/18/2023]
Abstract
The compact (cp) phenotype in cucumber (Cucumis sativus L.) is an important plant architecture-related trait with a great potential for cucumber improvement. In this study, we conducted map-based cloning of the cp locus, identified and functionally characterized the candidate gene. Comparative microscopic analysis suggested that the short internode in the cp mutant is due to fewer cell numbers. Fine genetic mapping delimited cp into an 8.8-kb region on chromosome 4 harboring only one gene, CsERECTA (CsER) that encodes a leucine-rich repeat receptor-like kinase. A 5.5-kb insertion of a long terminal repeat retrotransposon in the 22nd exon resulted in loss-of-function of CsER in the cp plant. Spatiotemporal expression analysis in cucumber and CsER promoter-driven GUS assays in Arabidopsis indicated that CsER was highly expressed in the stem apical meristem and young organs, but the expression level was similar in the wild type and mutant cucumber plants. However, CsER protein accumulation was reduced in the mutant as revealed by western hybridization. The mutation in cp also did not seem to affect self-association of CsER for formation of dimers. Ectopic expression of CsER in Arabidopsis was able to rescue the plant height of the loss-of-function AtERECTA mutant, whereas the compact inflorescence and small rosette leaves of the mutant could be partially recovered. Transcriptome profiling in the mutant and wild type cucumber plants revealed hormone biosynthesis/signaling, and photosynthesis pathways associated with CsER-dependent regulatory network. Our work provides new insights for the use of cp in cucumber breeding.
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Affiliation(s)
- Feifan Chen
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Jianpeng Yong
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Gaoyuan Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, Gansu, China
| | - Mengying Liu
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qiqi Wang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Huili Zhong
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yupeng Pan
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Peng Chen
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.
- USDA-ARS Vegetable Crops Research Unit, Madison, WI, 53705, USA.
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Wang S, Wang K, Li Z, Li Y, He J, Li H, Wang B, Xin T, Tian H, Tian J, Zhang G, Li H, Huang S, Yang X. Architecture design of cucurbit crops for enhanced productivity by a natural allele. NATURE PLANTS 2022; 8:1394-1407. [PMID: 36509843 DOI: 10.1038/s41477-022-01297-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/31/2022] [Indexed: 05/12/2023]
Abstract
Increasing production efficiency is a top priority in agriculture. Optimal plant architecture is the biological basis of dense planting, high crop yield and labour cost savings, and is thus critical for improving agricultural productivity. In cucurbit crops, most species have elongated internodes, but the path to architecture improvement is still not clear. Here we identified a pumpkin accession with a dominant bushy trait, and found that the associated Bush locus harbours a cucurbit-conserved cis-regulatory element in the 5' untranslated region of a transcription factor gene YABBY1. In cucurbit crops, various B-region deletions enhance the translation of YABBY1, with consequent proportional suppression of stem length in a dose-dependent manner. Depending on different cultivation patterns, the precise deployment of these alleles has significant effects on yield improvement or labour cost saving. Our findings demonstrate that the engineering of the YABBY1 B-region is an efficient strategy to customize plant architecture in cucurbit crops.
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Affiliation(s)
- Shenhao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Kun Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zheng Li
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Yangyang Li
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Jiao He
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Bowen Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tongxu Xin
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haojie Tian
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaxing Tian
- Beijing Vegetable Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Guoyu Zhang
- Beijing Vegetable Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Haizhen Li
- Beijing Vegetable Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Xueyong Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
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Chen J, Huang Y, Liu X, Chen G, Liu L, Cheng Z, Song W, Han L, Wang S, Wang L, Li M, Zhang X, Zhao J. CsIAGLU Regulates the Angle of Leaf Petiole by Affecting Endogenous Content of Auxin in Cucumber ( Cucumis sativus L.). Genes (Basel) 2022; 13:genes13122216. [PMID: 36553483 PMCID: PMC9777852 DOI: 10.3390/genes13122216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
The leaf angle is an important factor determining plant shoot architecture that may boost crop yield by increasing photosynthetic efficiency and facilitating high-density planting. Auxin is an important phytohormone involved in leaf angle regulation. Here, we identified two Single-Nucleotide Polymorphisms (SNPs) in the Indoleacetic Acid (IAA) glucosyltransferase gene CsIAGLU in 80 re-sequenced cucumber lines, of which the CsIAGLU717G,1234T is the dominant allele associated with a small leaf pedicle angle (LPA), whereas CsIAGLU717C,1234A is linked with a large LPA. CsIAGLU was highly expressed in leaves and petioles. In natural cucumber populations, the expression of CsIAGLU was negatively correlated with the LPA. The mutation of CsIAGLU induced by the CRISPR-Cas9 system resulted in elevated free IAA levels and enlarged cell expansion on the adaxial side of the petiole base, thus producing a greater LPA. Consistently, exogenous IAA treatment led to increased LPA and cell size. Therefore, our findings suggest that CsIAGLU functions as a negative regulator of LPA development via auxin-mediated cell expansion in cucumber, providing a valuable strategy for cucumber breeding with small LPAs.
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Luo C, Yan J, Liu W, Xu Y, Sun P, Wang M, Xie D, Jiang B. Genetic mapping and genome-wide association study identify BhYAB4 as the candidate gene regulating seed shape in wax gourd ( Benincasa hispida). FRONTIERS IN PLANT SCIENCE 2022; 13:961864. [PMID: 36161030 PMCID: PMC9493316 DOI: 10.3389/fpls.2022.961864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/06/2022] [Indexed: 06/16/2023]
Abstract
Wax gourd is an important vegetable crop of the Cucurbitaceae family. According to the shape and structure of the seed coat, the seeds of the wax gourd can be divided into bilateral and unilateral. Bilateral seeds usually germinate quickly and have a high germination rate than unilateral seeds. Thereby, wax gourd varieties with bilateral seeds are more welcomed by seed companies and growers. However, the genetic basis and molecular mechanism regulating seed shape remain unclear in the wax gourd. In this study, the genetic analysis demonstrated that the seed shape of wax gourd was controlled by a single gene, with bilateral dominant to unilateral. Combined with genetic mapping and genome-wide association study, Bhi04G000544 (BhYAB4), encoding a YABBY transcription factor, was identified as the candidate gene for seed shape determination in the wax gourd. A G/A single nucleotide polymorphism variation of BhYAB4 was detected among different germplasm resources, with BhYAB4G specifically enriched in bilateral seeds and BhYAB4A in unilateral seeds. The G to A mutation caused intron retention and premature stop codon of BhYAB4. Expression analysis showed that both BhYAB4G and BhYAB4A were highly expressed in seeds, while the nuclear localization of BhYAB4A protein was disturbed compared with that of BhYAB4G protein. Finally, a derived cleaved amplified polymorphic sequence marker that could efficiently distinguish between bilateral and unilateral seeds was developed, thereby facilitating the molecular marker-assisted breeding of wax gourd cultivars.
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Affiliation(s)
- Chen Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Jinqiang Yan
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Wenrui Liu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Yuanchao Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Piaoyun Sun
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Min Wang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Dasen Xie
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Biao Jiang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
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